Superhelical DNA Transition Analysis This web page provides users with access to four algorithms, which calculate the statistical mechanical equilibrium properties of various types of secondary structure transitions in a DNA sequence that is under negative superhelical stress. The SIDD algorithm analyzes the destabilization of the DNA duplex, which in its most extreme form involves strand separation. The SIBZ algorithm calculates the statistical mechanical equilibrium properties of the Bform to Zform transition in a DNA sequence that is under negative superhelical stress. The BDZtrans algorithm analyzes the competition between denaturation and BZ transitions. And the DZCBtrans algorithm analyzes the threeway competition between denaturation, BZ transitions and cruciform extrusion. This method uses an Inverted Repeat Finder algorithm developed by Gary Benson in 2004 (Genome Res.,14,1861). The details of the analytic methods used are available in the papers cited below.
The user may specify the base sequence to be analyzed, which can be either in FASTA format or in a file that contains nothing but the A, C, G, and T characters that comprise it. The user must specify whether the sequence is linear or circular. The default temperature and level of stress may be used, or specific values may be specified. The stress level is expressed as the superhelix density. This calculation slows considerably as the level of stress is increased, so it is not recommended to use superhelix densities beyond 0.08. The user also may specify which of the algorithms to run on their sequence.
The output of the SIDD analysis is twofold. First, G(x) is the denaturation energy, the incremental free energy needed to force the base pair at position x to be open. Stable sites have high values of G(x) while destabilized sites have low values. The second output is the probability p(x) of strand separation of base pair x. The outputs for the other transition types are their base pairspecific probabilities. The parameters used in the analysis and other quantities of interest are included in the output.
The output is available for downloading once the requested analysis has been completed.

Papers that present or use results calculated with this SIBZ algorithm should cite the following paper:
Zhabinskaya, D and Benham, C.J. (2010) Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA, PLoS Comput Biol 7(1): e1001051. 
Papers that present or use results calculated with WebSIDD should cite the following paper:
Bi, C.P. and Benham, C.J. (2004) WebSIDD: Server for Predicting Stressinduced Duplex Destabilized (SIDD) Sites in Superhelical DNA, Bioinformatics 20: 14771479. 